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mmu_circRufy1_646
Basic information of circular RNA
PanCircBase ID:
mmu_circRufy1_646
mm39_Chr. Position ID:
chr11|50305343|50312630|-
Gene name:
Rufy1
Transcript:
ENSMUST00000020643.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
7,6,5,4,3,2
Exon/intron offsets:
0,1723,2667,5104,5860,7113
Genomic length:
7287
Exon/intron sizes in nt:
6,66,21,24,10,21,18,170
Flanking exon/introns:
chr11:50301462-50305343|chr11:50312630-50321610
Splice length:
646
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_114773
Human Ortholog IDs:
Mature spliced Sequence:
CTTCCAAAGGCCAGATGATGGAGGAGCGTGCCAACCTAATGCACATGATGAAACTCAGCATTAAGGTCTTACTCCAGTCTGCCCTTAGCCTGGGACGCAGTCTGGATGCAGACTATGCCCCCTTGCAGCAGTTCTTTGTAGTGATGGAGCATTGCCTCAAACATGGGCTGAAAGTCAAGAAGAGTTTCATTGGCCAAAATAAGTCTTTCTTTGGTCCTTTGGAGCTGGTGGAAAAACTTTGTCCTGAAGCATCAGATATAGCTACCAGTGTCAGGAATCTTCCAGAACTAAAGACAGCCGTGGGAAGAGGCAGAGCGTGGCTTTATCTTGCTCTCATGCAAAAGAAACTGGCAGATTATCTGAAAGTCCTCATAGACAACAAGCAGCTCCTAAGTGAGTTCTATGAGCCCGAGGCCTTAATGATGGAGGAGGAAGGAATGGTGATCGTGGGTCTGCTGGTGGGACTCAACGTTCTGGATGCCAACCTCTGCTTAAAGGGAGAAGACTTGGATTCTCAGGTCGGGGTGATTGACTTCTCTCTCTGTCTGAAGGACGCACAGGATCTTGACAGCGGCAGAGAGCATGAAAGAATTACCGATGTCCTTGATCAGAAAAATTACGTGGAGGAACTTAACCGGCACCTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGACGCACAGGATCTTGACA
60.04
GGGCAGACTGGAGTAAGACC
59.46
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATCTTGACAGCGGCAGAGA
59.83
GGGCAGACTGGAGTAAGACC
59.46
170
PCR template sequence:
TGAAGGACGCACAGGATCTTGACAGCGGCAGAGAGCATGAAAGAATTACCGATGTCCTTGATCAGAAAAATTACGTGGAGGAACTTAACCGGCACCTAAGCTTCCAAAGGCCAGATGATGGAGGAGCGTGCCAACCTAATGCACATGATGAAACTCAGCATTAAGGTCTTACTCCAGTCTGCCCTTAGCCTGGGACGCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-miR-298-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCGGCACCTAAGCTTCCAAAGGCCA
siRNA sets
CTTTGGAAGCTTAGGTGCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRUFY1_646_ORF_1
1.28
0.23026368
0.955683353
696
ORF sequence:
ATGATGGAGGAGCGTGCCAACCTAATGCACATGATGAAACTCAGCATTAAGGTCTTACTCCAGTCTGCCCTTAGCCTGGGACGCAGTCTGGATGCAGACTATGCCCCCTTGCAGCAGTTCTTTGTAGTGATGGAGCATTGCCTCAAACATGGGCTGAAAGTCAAGAAGAGTTTCATTGGCCAAAATAAGTCTTTCTTTGGTCCTTTGGAGCTGGTGGAAAAACTTTGTCCTGAAGCATCAGATATAGCTACCAGTGTCAGGAATCTTCCAGAACTAAAGACAGCCGTGGGAAGAGGCAGAGCGTGGCTTTATCTTGCTCTCATGCAAAAGAAACTGGCAGATTATCTGAAAGTCCTCATAGACAACAAGCAGCTCCTAAGTGAGTTCTATGAGCCCGAGGCCTTAATGATGGAGGAGGAAGGAATGGTGATCGTGGGTCTGCTGGTGGGACTCAACGTTCTGGATGCCAACCTCTGCTTAAAGGGAGAAGACTTGGATTCTCAGGTCGGGGTGATTGACTTCTCTCTCTGTCTGAAGGACGCACAGGATCTTGACAGCGGCAGAGAGCATGAAAGAATTACCGATGTCCTTGATCAGAAAAATTACGTGGAGGAACTTAACCGGCACCTAAGCTTCCAAAGGCCAGATGATGGAGGAGCGTGCCAACCTAATGCACATGATGAAACTCAGCATTAA
Peptide sequence:
MMEERANLMHMMKLSIKVLLQSALSLGRSLDADYAPLQQFFVVMEHCLKHGLKVKKSFIGQNKSFFGPLELVEKLCPEASDIATSVRNLPELKTAVGRGRAWLYLALMQKKLADYLKVLIDNKQLLSEFYEPEALMMEEEGMVIVGLLVGLNVLDANLCLKGEDLDSQVGVIDFSLCLKDAQDLDSGREHERITDVLDQKNYVEELNRHLSFQRPDDGGACQPNAHDETQH
IRESfinder result
IRESfinder score
0.597016795
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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